Flow cytometry – experimental design and sample preparation

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​​Tips for selecting controls and preparing samples for flow cytometry.

Flow cytometry is a valuable technology in modern biomedical research. It is widely used for the characterization of cell populations and expression analysis of protein markers. However, poor experimental design may render your results useless. This article is dedicated to provide you with valuable tips to set up your experiment and prepare your samples.

Experimental design - a thorough approach will pay off

Research what is available in the literature, specifically in relation to your sample and experiment. Groundwork will avoid mistakes further down the road.

Make sure your instrument is suitable for the detection of the fluorophores you decide to use. You want fluorophores with maximum brightness and minimum spillover. Try our new Alexa Fluor® conjugated secondary antibodies validated for flow cytometry.

Make sure you have all the reagents you need in excess. Prepare a step-by-step protocol and calculate the amounts of reagents required for your number of samples.

You may want to use a marker of dead cells as their presence can significantly affect your analysis. Various assay-compatible dead cell markers are now available.

Titrate your antibodies to find out the optimal dilution and minimize background. The working dilution provided in the datasheet can be used as a starting point.

Do your research to determine what to expect. For instance, cell lines are relatively homogenous while primary cells usually consists of a heterogeneous population of different cell types.

Sample preparation

Use BSA or FBS as a blocking agent to minimize non-specific binding.

Use Ca/Mg++ free buffers to prevent cation-dependent cell adhesion. You can add up to 5 mM EDTA to further prevent cell adhesion. Under these conditions, BSA (0.1 – 1%) or dialyzed FBS (1 – 5%) should be used as non-dialyzed FBS would replace the Ca/Mg++.

For live cells, internalisation of cell surface proteins can be prevented by performing all steps on ice. Chill reagents at 4°C before use. Gentle detachments methods may be required for adherent cell lines as trypsin can induce internalisation of cell surface proteins.

It is very important to obtain a single cell suspension to avoid clogging up the system. Filter your samples before the run with cell-strainer caps if possible. Use a nylon mesh only as a last resort as you may lose many cells with this system.